The Chronicles of the Colonial Survivors
by The Wrath of the Ancients
Summary: AU. The survivors of the colonies find three more Battlestars. Will they succeed in saving the remainder of the human race?
1. The Would have been Queen Cain

**The Would have been Queen Cain Dethroned **

AU set during _Pegasus,_starting at the scene were Adama is about to fire on Cain for the kidnapping of his officers and announcing her wish to murder them.

* * *

><p>The <em>Vipers<em> hovered in formation between the two _Battlestar_'s ready to attack if either of the Commanders gave the order.

"Adama this is your last chance," Rear Admiral Cain pleaded over the radio. "Stand down and I'll drop the charges against you and your bridge crew."

"And why should I believe you," Adama countered.

"Colonel Tigh you are herby ordered to relieve Commander Adama of duty and to stand down your _Vipers_" Cain gave up trying to reason with Adama.

"Like Frak," Tigh practically shouted down the comms link. "I'm not following orders of some war _criminall!"_

* * *

><p>Just as the <em>Pegasus Viper<em>'s were about to attack ,another _Mercury_-class _Battlestar _came out of FTL just in front of them, it was quickly followed by two other _Battlestars_, both the same class as _Galactica_.

On the _Galactica's _CIC chaos had erupted as the three Colonial ships appeared.

"This is _Zenobia-Actual, _Admiral Walter commanding," Admiral Watter said over the communications from his flagship. "We've monitored your situation, stand by."

* * *

><p>On the far cleaner and slightly more advanced bridge of the <em>Zenobia<em> Admiral Walter turned to on of his officers, "Get me Rear Admiral Cain on the line" He said while raising the telephone to his face. "Rear Admiral this is Admiral Walter speaking on behalf of the Battlestars_ Zenobia, Challenger _and_ Logopolis, _authenticate immediately."

"This is _Pegasus_-actual, Rear Admiral Cain commanding, sending over authentication codes, now" Cain said clearly frustrated that someone of a higher rank had showed up.

"Authentication acknowledged, Rear Admiral Cain you are ordered to hand over Chief Tyrol and Lieutenant Agathon to the _Galactica, _and then send over a copy of your logs for review, is that clear Rear Admiral Cain" Walter said much to the horror of the _Pegasus _crew and delight of the _Galactica_'s crew.

"Order not acknowledged, Admiral Walter," Cain said trying to express her self-absorbed superiority complex.

"You will follow orders or your ship will be fired upon," Admiral Walter told Cain, he then turned to his communications officer. "Signal the _Challenger, Logopolis _and _Galactica, _tell them to target the _Pegasus_."

* * *

><p>On the <em>Pegasus<em> a shrieking alarm activated, Hoshi turned round and looked at the now illegal admiral Cain. "Radiological alarm, all four Battlestars have armed nukes and are targeting us, Cain took a deep breath and gambled.

"You won't fire, not if you want the _Galactica _officers alive." She said smiling.

"Yes we will, none of us count our kills because of the simple fact that we don't need to, my crew and that of our escorts have won against two hundred Cylon Baseships, with a little help from a Cylon defector, I promise you the _Pegasus _is severely outgunned." Admiral Walter told her while trying to warn her. "Just against the _Galactica_ you could probably win, but you wouldn't have a ship left, against my ship you'd loose, but against all four of us you don't stand a chance, come on, even a jumped up little girl with connections like you can see that, there's no way you can win, so stand down."

Cain looked around her bridge crew and realised that she was beaten, she leaned down to the centre table before turning to Hoshi, "Signal our surrender and return the _Galactica_ officers and call back our _Vipers_." She glared up at the DRADIS screens and turned to go to her quarters.

* * *

><p>"Commander Adama, I'd like you to supervise the arrest of the marines who assisted Lieutenant Alistair Thorn in his sexual assault of the Cylon prisoner of war on their ship, if they resist you have my permission to shoot to stun, I will be coming over in one hour please have the President onboard, oh and Commander there's no need for your crew to wear dress uniforms if you don't want to, to be honest I'd prefer your crew didn't, it saves time and I don't care much for protocol, I just care about the law, <em>Zenobia <em>out."

* * *

><p><em>So, how do you like it, Admiral Walter's crew will be named later on and there back story will be far opposite the Pegasus' voyage, also see if you can guess who the defector is.<em>


	2. Building Bridges

**Building Bridges**

_Follows the events of Pegasus._

Admiral Walter's _Raptor _entered the _Galactica_'s shuttle bay, following orders Adama had brought the President back over and none of his crew were in dress uniforms. When Admiral Walter exited the _raptor _he looked around and smiled slightly nostalgically as he had once served aboard a _Columbia _class Battlestar before.

"Admiral on deck," one of the marines shouted out as the men stiffened and stood to attention.

"At ease," Walter said with a smile before stepping off the ramp and walking in front of Commander Adama. "Commander Adama, it's a pleasure to finally meet you," The two military officers shook hands the Walter turned to the President, "Madame President Laura Roslin, I presume," He said as a bit of a joke to break some ice between the crews who both laughed and released some tension, "It's a pleasure." And the both shook hands before turning to the rest of the _Galactica's _crew, and dismissed them.

Admiral Walter, President Roslin and Commander Adama sat in his office around the table, Walter took a deep breath and began his tale of how the _Zenobia, Challenger _and _Logopolis _had survived the Cylon attack.

"The _Zenobia _was on a deep space exploration mission," he began. "We FTL jumped in to an unchartered system, as soon as we got there the ships systems began to overload, we first thought it was sabotage but we then found a low level energy field surrounding the star system, it was causing all of the overloads. After a few days we found no way to block the signal we found a ship on the DRADIS, it was a Cylon baseship, well what was left of it, they were sent there to ambush us but had been affected by the same energy field that had disabled us, when we got there our main engines blew out, we boarded the cylon ship, it had lost life-support and it's power core was completely useless, after searching we found two humanoid cylons a six and a five, we brought them back to the _Zenobia_ were they told us that they had traced the energy field to one of the planets in the solar system."

" I offered them a truce, essentially a straight swap, we get their engines and data on the system and in return when we leave the system we drop them off at a Cylon base, the alliance worked we escaped and the cylons admitted the truth to us, but to the Cylon's surprise I kept my word and dropped them off and found the _Challenger _dead in space, we were able to bring the ship back from the dead, but it was too late for the crew, we re-staffed the ship from my crew, shortly after that we tracked the transponder of the _Logopolis_, their crew had survived." Walter took another deep breath clearly struggling with the next bit.

"We found fifteen civilian ships, they were stripped of FTL drives and most of their crews had been illegally drafted by Cain who ordered the murder of the families of any selectees who didn't comply, we began to evacuate the survivors to our ships, then ten Cylon base ships showed up, I tried to evacuate them all until my XO ordered an FTL jump out of there, we only lefty fifty behind, which is still too high," a single tear fell from Walter's face. "That's why Cain's out of the service; I don't care if the Cylons get their hands on her, after what she's done."

Adama and Roslin smiled at the thought of Walter's efforts to save as many civilians as possible, "I suppose that's my one personal flaw, I can't compromise, I have to save everyone or I've lost." Walter added as he slumped into the chair, he sighed and used both hands to wipe his face before he looked at them and returned their smile.

"Now, that's enough about me, tell me about your fleet, it must be so satisfying to know you've saved so many thousands of people…"

The _Galactica _officers were once again having a party to celebrate the arrival of the three other Battlestars, Chief Tyrol was in the vicinity but was refusing to join the festivities because of his experience with the _Pegasus_ crew.

"Chief," a voice said from behind him, he twirled around to see Admiral Walter standing behind him. "I've just come out of a meeting with the President and Commander Adama, they told me you had a romantic relationship with the number eight sleeper agent Cylon known as Sharon 'Boomer' Valerii until the XO ordered you to break it up,"

"Look, I didn't know she was-"Chief Tyrol quickly said in response.

"It's alright," Walter cut him off. "I believe you; I understand that's why you went to defend the different version of Sharon in the brig at the moment,"

"Yeah, it's so hard, she looks like Boomer, but she acts differently, she's got a completely different personality, although no one else seems to notice it" Tyrol admits while looking down at the floor.

"You know why you were the only person who found her personality different?" Walter asked Tyrol. "It's because you're the original version's lover, you were closer than anyone else, and you noticed the differences because you knew the original so well, and that's what I needed to know, I'll need you to come aboard the _Zenobia_, but after the battle we need you focused for that."

"Carry on Chief, and do me a favor," Walter started before gesturing to the party. "Feel free to join the festivities."

Admiral Walter left the room and headed towards the exit, while Galen Tyrol smiled slightly at a torrent of memories of his time with the original Sharon Valerii, until he remembered what he said to her in that cell and then the memory of her body falling back into his arms reeling from Cally's gunshot, he started to cry before wiping his eyes and focusing on the good memories of his past with her, he then joined the party being careful not to make eye contact with anybody, especially Cally.

_Nice train of thought about Caprica-6, and you're right if it was Boomer she technically wouldn't be a defector._


	3. Assault on the Resurrection ship

**Assault on the Resurrection Ship**

_Follows the events of Resurrection ship_

"Madam President no," Admiral Walter told Laura Roslin in response to her query. "I will not murder Helana Cain."

"But as you've said she's a danger to the civilians in the fleet, and needs to be removed from the equation," Roslin countered.

"Madam President, that's exactly why Cain's going on trial for war crimes and violation of the Colonial Convention for Treatment of Civilians and Prisoners during war time, and the penalty will be life imprisonment and being booted out of the service," Walter told her. "She'll be arrested after the attack on the resurrection ship, now if you'll excuse me."

Admiral Walter turned and left the President's office on Colonial One and entered his _Raptor_ to return to the _Zenobia_ to plan the attack on the Resurrection ship.

"We use the _Pegasus_ and _Galactica_ to engage the Cylon baseships while Lieutenant Thrace takes the _Blackbird_ to nuke the target," Colonel Longman presented her plan to the gathering of Commander Adama and Colonel Fisk.

"I still don't understand while I'm here instead of Admiral Cain," Fisk said turning to Walter and Adama. "Admiral Cain's in command of the _Pegasus_, not me."

"Not any more, _Former Rear Admiral _Cain has been arrested and relieved of duty, and after the battle will be put on trial by the Judge Advocate General, who happens to be aboard my ship, the charges are murder, violations of both the Colonial Convention for treatment of civilians and Prisoners of war." Walter told him.

"Cylons aren't humans, they're just frakkin' toasters! They have no rights," Fisk shouted at them.

"Not necessarily," it was Adama who responded. "At the end of the first war by negotiating a treaty the government technically awarded them sentience, as you can't negotiate with a machine, so they must be sentient, and the JAG officer who has become the Judge Advocate General as per protocol after convening a hearing judged that human form Cylons are sentient and have rights and are protected by the previously mentioned convention."

"Suffice to say Colonel, pretty much all of the _Pegas-_ your crew are on thin ice with multiple charges of rape and sexual assault and illegal conscription of civilians into the military," Admiral Walter told him as he got up from his chair and looked into Fisk's eyes, a dark glimmer flashed in his eyes and Fisk clearly trembled. "A certain Lieutenant Hoshi is the only person with absolutely no charges against him, now get out of my office and prove that your crew is not beyond redemption, dismissed!"

Fisk all but ran out of the office clearly terrified.

"Commander Adama, keep an eye on Fisk, he might try something with just the _Galactica _there," Walter advised him. "Also I'm out fitting the _Galactica _with two of the prototype 'Starship buster' 150 gigton nukes, keep your finger on the trigger, and good luck," Walter shook Adama's hand before he left.

Walter lingered in his office leaning on his chair, his face deep in contemplation, before bursting out of the chair and sprinting to the CIC to send the two Battlestars off on their battle.

A few hours later both Battlestars returned to the fleet intact and ready to move on while reporting a mission success.

Walter stood at the centre table of the _Zenobia_'s CIC and gave the order for the FTL jump beyond about 20 light years to throw off the Cylon's scent on them.

_Sorry another short one, I couldn't see any method of continuing this chapter, it seemed to have ended quite nicely and it seems pointless to add anything else to it. _

_Next chapter may be a flashback or maybe Tyrol's journey to the Zenobia._


	4. Mutinies, Truths and a New Beginning

**Mutinies, Truths and a New Beginning**

Chief Tyrol and Admiral Walter boarded the _Raptor_ bound for the _Zenobia_, Walter looked up at Tyrol,

"So you've served on ships since you were eighteen?" Walter asked.

"Erm, yeah, why?" Tyrol answered before quickly adding "sir."

"Oh, nothing, just wondering why you never got a commission, with your experience you could easily be an engineer, or even deputy of the Corps of Engineers, why stay enlisted." Walter asked.

"I don't know, I guess I just never got around to it," Tyrol said while looking down.

"Liar," Walter said. "I was a psychiatrist before joining the military, I can tell when you're lying, now please tell me the truth."

Tyrol sighed, "I was offered a commission a few months before the decommissioning, but I err… didn't take it"

"Because of Boomer," Walter asked while already knowing the answer.

"Yes I was planning to propose to Sharon and leave the service; we planned to build a house on Picon." Tyrol's eyes were slightly nostalgic and he was beginning to cry.

"It'll all be alright," Walter said while looking at Tyrol with concerned eyes.

"No it's not, no matter how hard I try I can't stop loving her despite everything that's happened," Tyrol said while looking down.

"Then why didn't you press charges on Specialist Cally?" Walter asked now interested in the way Galen Tyrol was able to forgive the woman who murdered the love of his life.

"I don't know, the more I go over it the more I wish I did press charges but I didn't I… I just don't know why," Tyrol said as he began contemplating the question.

"Well I can think of three answers, answer one; you didn't want to loose a valuable member of your team, two you think of Cally as a little sister who you wanted to protect from as misguided sense of loyalty to a type of family or answer three, after learning about resurrection you held out hope that she would have been resurrected and would one day find a way back to you and you didn't charge Cally because that would mean you had conceded the point that Sharon had been killed and this would be like defeat." Walter told him a little patronisingly.

"Admiral with all do respect can you stop psycho-analysing me, I find it strange," Chief Tyrol told the Admiral.

"So, which of my theories is it?" Walter asked looking directly into Tyrol's eyes.

"Three, I guess," Tyrol's eyes began to mist up and a tear fell down his cheek. "I just didn't want to admit I'd lost her."

"And now?" Walter asked as he lent forward.

"Still, I just can't move on, I love her, do you get that I'm in love with the woman who shot the commander I view as almost a father?"

"As I understand it she didn't shot him, it was the post-hypnotic programming entered into her brain after she destroyed a baseship therefore becoming a threat to the Cylons, so they neutralised her as a threat and temporarily neutralised Adama as the commander in charge of military forces."

"Wait a second, why aren't you calling her a traitor, or a toaster, or a skin-job." Tyrol asked now more confused than ever.

"Well a toaster is a device used to make toast and as I recall there were never actual Cylons designed to be toasters so I don't quite understand why people called them toasters, and looking at all the evidence it's clear that she had no idea why she shot Adama and quite frankly skin-job sounds a little rude." Walter said.

"_This is Admiral Cain of the Pegasus you will stand down or be destroyed," _a female voice announced over the communications.

Walter didn't wait a single second before springing into action and leaning into the forward section and looking out of the forward and at the _Pegasus _which was coming into weapons range and was arming it's weapons and launching _Vipers_, Walter looked back at Tyrol and asked one question…

* * *

><p>Colonel Longman looked around the CIC of the <em>Zenobia<em> and swore, she turned to the communications officer.

"How the frak did Helena Cain get out of the _Pegasus _brig?" She asked as she turned back to look at the DRADIS display. "And tell the civilians to get to a safe distance, that frakkin' bitch better be smarter than she looks or we're gonna have to destroy the _Pegasus_ today..."

* * *

><p>"Initiate jamming now," Walter told Tyrol who was standing at the computer console in the back, before turning back to pilot. "Take her in nice and slowly, please nobody look out of a window."<p>

* * *

><p>Lieutenant Hoshi prided himself at trying to be the best senior watch officer in the fleet, he also liked to be on the right side of the law, and sometimes he compromised those principles if the price was high enough, but not today. He looked round at the bridge, Colonel Fisk's dead body lay on the floor, Louis Hoshi wondered how this had happened before remembering; Helena Cain had somehow managed to convince some marines to let her out of the brig and she had proceeded to order them to murder Fisk and anyone who resisted her authority, and now it was his turn.<p>

"Last chance Mr Hoshi," Cain said while levelling the gun at his head.

Hoshi knew this was probably going to be his last moments, he had to make them count, he had to try to get through to her, make her reconsider. "With all due respect Ms Cain, this is probably yours, Walter with have your guts for boot laces,"

Just as Cain was about to fire the bridge rocked to the side and some of the computers overloaded and exploded showering the bridge with shratnel and flames, the communications speakers activated.

"This is Admiral James Walter acting Commander in Chief of Military forces to _Pegasus, _surrender or you will be fired upon." Cain looked up at the DRADIS screen and groaned as she saw that it was useless because of interference, so she had no idea of the location of Walter's _Raptor_, which was right below the _Pegasus_ external FTL coolant vent, with two armed missiles ready to fire.

"This is _Pegasus-_actual, I don't know where you are but I highly doubt you can do any substantial damage."

* * *

><p>"Deactivate the DRADIS jamming," Admiral Walter ordered Chief Tyrol before turning back to the forward window and smiling.<p>

* * *

><p>Cain's presumptuous victories smirk disappeared when the DRADIS was able to get a clean fix on the <em>Zenobia<em>, right in front of the ship, the _Rapter,_ just above the external FTL coolant vent and the position of the _Galactica_, right behind the engines. When Cain looked down she saw the same fear in her crew's eyes, they were terrified that she would order an attack on the two Battlestars and start a battle that she couldn't possibly win.

"Grr! Alright we surrender," Cain grated at Admiral Walter.

"You will present yourself on Colonial One in two hours, no aides." Walter responded, his intention to arrest her personally clear to everyone in the _Raptor._

**Colonial One**

**President's office**

**13:00**

"Helena Cain, I am placing you under arrest for murder and war crimes, you may not say anything at this time but anything you do say will be used as evidence in court of law during your trial." Walter said while placing handcuffs on her. "You will be taken from here to be held in the _Zenobia_ brig until your trial were sentence will be carried out."

Walter then pulled her out of the office and into the _Raptor,_ he turned to a marine who had stayed inside, "If she moves, shoot with tranquiliser rounds," he then made his way into the cockpit of the _Raptor_. He pulled on a headphone set with an added microphone.

"This is _Raptor_-498 en route to Battlestar _Zenobia_, _Lonely God_ piloting, permission to depart?" Walter asked the pilot of the Presidential vessel.

"This is _Colonial One_ please verify call sign," The pilot ordered.

"This is _Lonely God_, call sign verified,"

"_Lonely God, _this is _Colonial One, _you are cleared to depart,"

"Acknowledged, departing now."

**Battlestar Zenobia**

**Starboard Hanger Deck **

**13:15**

Admiral Walter exited the _Raptor_ to see Galen Tyrol helping out the _Zenobia's _deck crew Walter smiled and looked at him,

"You just could stand by and do nothing?" he asked rhetorically while gesturing to some marines to take Helena Cain away.

"Well you left me here two hours ago with instructions to wait I got bored so I asked your deck chief if he needed any help." Tyrol said shrugging.

"It's alright, any way you're probably wondering why I brought you here."

"Yes, kinda,"

"Well there are two reasons; one I need you to check a theory of mine and two is a special weapon onboard which we're having trouble with," Walter told him. "We're going to the weapon first and my theory later."

"Why did you say it the other way round?"

"I don't know, it was just the way I thought about it," Admiral Walter said while leading them further into the ship.

* * *

><p>Couples in the story that I'm going to use for definite:<p>

Boomer/Chief (This will become an important relationship, with perhaps a wedding in the future)

Athena/Helo (A Canon relationship I'm keeping)

Dee/Billy (Billy will not be dying in this story)

The issue I'm having is what to do with Laura Roslin and Gina Inviere (who will be sticking around)

Here's what I'm thinking:

Roslin/Lee (because Roslin/Zarek is just, shudder and I don't want Adama with her in this, I don't know why)

Gina/? (Any suggestions, other than Gaius Baltar, who I'm thinking of paring up with Tory)


	5. New Weapons, the Corps of engineers and

**New Weapons, the Corps of engineers and a cure for cancer**

This Chapter will start to cover the events of Epiphanies, Black Market and start to cover Scar

* * *

><p><strong>Battlestar Zenobia<strong>

_**Exact Location Classified**_

**Colonial Corps of Engineers**

**13:30**

Admiral Walter placed his hand on the palm print system, he waited a few minutes until the doors parted, and he gestured for Tyrol to follow him in.

The dark room began to light up, showing computer consoles in a circular formation around four chairs and two large television monitors opposite the door, one split into six split screens showing the space outside of the _Zenobia_, while the other screen showed a virtual diagram of some sort of weapon.

Walter reached behind him to shut the door; he then turned back to Tyrol.

"Chief Tyrol, everything behind this door is classified beyond top secret, you are the first enlisted person to gain access to this room," Walter told him, all sense of any emotion gone from his face. "How does that feel?"

"Well... I feel honoured sir."

"Good," as Walter responded to Tyrol's sentence he smiled again. "Anyway, this is the control room for a prototype weapon, which instead of relying on any type of physical ammunition uses electromagnetic waves as offensive weapons; the whole point was to send a precisely modulated pulse to disable machinery, like taking out a whole enemy ship without wasting any ammo, you can then board and evacuate the survivors, however so far we haven't been able to make it work"

Walter turned and allowed Tyrol access to the systems and controls where he studied them before he began to work, "You see there's the problem…"

**Battlestar Challenger**

**Main Engine Room**

**13:30**

Colonel Scott prided himself as being one of the best engineers on the _Challenger _and as such he knew that what the vice-president had just asked was impossible.

"Now with all due respect Mr Vice-President I can't give you the blueprints for the enhanced FTL drive or the FTL computer, it's classified; now get out before I have you thrown out,"

Baltar turned and left as Scott turned back to the engine, "Vol get me Admiral Walter,"

**Battlestar Galactica**

**Morgue**

**13:35**

The _Zenobia's_ medical officer Dr Tolian Naros stood next to his _Galactican_ counterpart.

"We think that there is an implant that contains the _Cylon _programing, once that is removed they should be just a cover personality," Tolian told his counterpart.

"Well this would have been useful if we'd known about it beforehand, but as you can see, she's dead," Cottle said in response.

"Yes, I can see that but, we could still check the intell," Naros countered.

"Alright, let's get the body to sickbay and test your little theory,"

**Battlestar Zenobia**

_**Exact Location Classified**_

**Colonial Corps of Engineers**

**14:30**

After hours of working Tyrol had been able to track down the problem with the EM pulse weapon and together with a team of engineers had corrected it, now they were ready to test it.

"_Viper_ 895 ready,"

"_Raptor _654 standing by,"

"Fire" Walter gave the simple order.

The weapon fired a bluish energy pulse which disabled all of the electronics on the _Viper_ and the _Raptor_ crew was able to recover the pilot and the _Viper_, in the end it was a successful test.

**Battlestar Galactica**

**Medical Bay**

**14.30**

After a few hours of working the two doctors had removed the pen sized implant from the dead Sharon's brain, they had had to cut through a lot of dead brain tissue and while it confirmed the theory about how sleeper agents worked it also proved that it was nearly impossible to remove it.

"Well there goes any hope of removing it," Cottle said sarcastically while looking down at the body.

"We'll find a way, we'll have too." Naros cryptically said before he left the sickbay.

**Battlestar Zenobia**

_**Exact Location Classified**_

**Colonial Corps of Engineers**

**14:30**

"Chief Tyrol, how long will it take for you to submit the full schematics for the Blackbird into the Corps of engineers personnel in the fleet," Admiral Walter said while walking towards him.

"Erm… I don't know why?"

"Because it worked very well and I'd like to replace the one we lost in the battle,"

"I see, I don't have any actual schematics ready,"

"We'll as soon as you get some spare time write them down, that's an order"

**Battlestar Challenger**

**Engineering**

**14:35**

"No, I can't give you the schematics Mr Vice-President; you're neither qualified nor cleared to look at them so get out of my engine room before I have you thrown out." Colonel Scott repeated once again to the Dr Baltar, he had quite clearly had enough. "Now you heard me, now get out."

Baltar finally decided to leave the _Challenger's_ engine room and left Colonel Scott to get back to work.

**Colonial One**

**Presidents Office**

**14:35**

"Let me get this straight, you want to put Chief Galen Tyrol in charge of the _Colonial Corps of Engineers_," Commander Adama asked the Admiral who was currently the _Acting _Commander-in-chiefof Colonial military forces.

"Yes, I do have a former head as chief engineer on the _Challenger_, but only he knows that ship inside out, and the _Challenger_ would barely function without him, and the next most experienced officer I could find, well… technically not an officer, but you can understand what I mean," Admiral Walter told the _Galactica's _commander.

"Well what did he say about it," Adama asked.

"I don't know, I haven't asked him yet, I thought I'd clear it with you first," Walter told him.

"Well okay, if he accepts the job he becomes the head of the Corps of Engineers,"

"Very well," Walter started before saluting. "Madam President, Commander.

**Battlestar Zenobia**

_**Exact Location Classified**_

**Colonial Corps of Engineers**

**15:00**

"How would you like to be the head of the Colonial corps of engineers?" Walter asked.

"Well, er I'd love to be, but don't you have to clear this with Commander Adama?" Tyrol responded.

"I already have, so is that a yes,"

"Yes sir,"

"Very well enlisted personnel can't be put in charge of a department, so I'm giving you a field commission of Colonel.

Tyrol blinked a few times, before thanking the Admiral, Walter then turned to leave before he turned back and handed Tyrol a large number of personnel files.

"Go through these files and chose your staff, I'll be back later."

**Battlestar Zenobia**

**Sickbay**

**15:15**

Admiral Walter walked into the main sick bay and looked around for his chief medical officer before turning to see the bed to his right, on it was the cylon number six recovered from the Pegasus. A number of her cuts and scars were covered in a sticky blue substance, it was an experimental formulae designed to accelerate cell regeneration; while it hadn't been chemically tested it worked.

"Ah, you're here," Dr Naros said while turning the corner.

"What's the prognosis Doctor?"

"Well that bastard got her pretty good, while we can heal her physical injuries, the erm, mental injuries will take longer, and she'll need extensive help, but I think that she'll recover."

"Good, how's house guest number one?"

"She's fine, and ever since she found out what's happening she's been excited, I think it's time you introduced them,"

"I was just thinking the same, carry on Doctor,"

**Battlestar Zenobia**

_**Exact Location Classified**_

**Colonial Corps of Engineers**

**15:30**

"I've been through these files and I think I know who to pick for the corps, but where will the headquarters be; on Zenobia or Challenger?" _Colonel _Tyrol asked.

"Actually I was thinking the Galactica," Admiral Walter said in response. "It's the oldest ship and needs the most help.

The brought a smile to Tyrol's face.

"Now let's get your new uniform."

**Battlestar Zenobia**

**High Security Observation cell**

**15:45**

Admiral Walter looked down into the cell as the two lovers were reunited, in a tearful manner, Walter smiled as they kissed.

"Theory confirmed," Walter's voice boomed through the overhead speakers. "You're definitely the same Sharon Valerii who was on Galactica, I can spot a fake couple from a mile away, I'll just clear you're re-admittance files _Lieutenant_ Valerii, for now have fun" Walter then left the observation deck and headed to the regular brig, he wasn't looking forward to this, not one bit…

"I've missed you… a lot," Tyrol stated between kisses, they both moaned as they sat on the bed ready for what was going to happen next…

**Battlestar Zenobia**

**Brig**

_**Temporary Residence of Helena Cain**_

**15:50**

The charges are murder, illegal drafting and treatment of civilians, an example would be the Scylla and the kidnap and attempted murder of Galen Tyrol and Karl Agathon. Ms Cain, do you know how much trouble you're in?" James Walter said looking down into her cell. "Do you know what, I don't blame the Cylons for whipping out the Colonies, they're like a storm, and you don't blame storms do you, what I blame is you, for stripping those civilians, they needed protection, instead you slaughtered them.

"It was war time I didn't have a choice, it wasn't me,"

"You know that's what angers me the most, you denying your crimes, for gods sake, IT WAS YOU!" Walter bellowed at Cain with his finger pointing at her, at Cain's down cast look, Walter continued. "Well look at that, perhaps the old girl's loosing the taste for the sport," Walter smiled briefly before leaving, hoping he had gotten through to her.

**Battlestar Galactica**

**Decks 21-24, Sections 21-25**

**Headquarters of Colonial Corps of Engineers under Colonel Tyrol**

_**Seven Days later**_

Knock, knock.

Tyrol looked up at the mahogany wood door into his office, he yelled for the person to enter, he was surprised to see Commander Adama walk into the room.

"Enjoying your new job, _Colonel,"_ Adama asked while gazing around at the office. "What's the mahogany wood substitute?"

"Well, it's actual wood, Colonel Scott on the Challenger said he'd do me a favour when he asked what decorations I'd want in my office I joked with mahogany wood, then I find out that he's had Boomer ferrying some of the last mahogany wood in the universe over to be installed in my office,"

"We'll, that's what I'm here to ask you about, Boomer," Adama started before sitting down. "You know this could take some getting used to, ah, right the thing is currently Lee won't have Boomer doing anything other than so called milk-runs for your department, so next time there's a major crisis she needs to volunteer to help out to win people's trust before they'll let her back into the squadron, any way I'm due for a meeting with the President and the Commander-in-chief, and if Colonel Scott has any spare wood can you get me some," Adama said before turning and leaving.

**Battlestar Galactica**

**War Room**

**Meeting with President, Admiral James Walter, Vice-President and Commander Adama**

"So we need to figure out what to do with this child," Roslin said from her death bed, this immediately angered Admiral Walter.

"Do with it! It's a child, madam President if you make any move to kill this child I will arrest you on charges of attempted infanticide, I won't give a dam about your condition, it's a child and you're not above the law," Walter passionately ranted to all who would listen.

"I agree with Walter's position," Baltar told the others.

"Now madam president if you make any move to kill that child I will personally see to it that you face trial before you die, is that clear," Walter firmly told Roslin. "The next item on the agenda is Lieutenant D'Anna Biers report from the Pegasus tribunal,"

"I still don't see why you trust her judgement, she's still a cylon," Roslin told anyone who would listen.

"It doesn't matter what you think, I've got her report here, most of the crew will be demoted back to the lowest ranks possible, Specialists Gage and Vireem will be confined on the Astral Queen along with Lieutenant Kendra Shaw, the only unaffected crew members are; Lieutenant Kara Thrace CAG, Lieutenant Louis Hoshi and Colonel Garner Chief Engineer," Walter summarised while reading the report.

"The next thing we should discuss is the Diamond Peace movement," Adama started.

"Oh," Walter groaned.

"They claim that two cylons switching to our side proves that we can be allies with them,"

"Have they ever heard that the exception is not the rule, arrest them, terrorist acts will not be tolerated."

**Colonial One **

**The next day**

"I want to thank you Admiral, if it wasn't for you I would have killed an innocent child," Roslin told the Admiral.

"And yourself," he quietly added.

"You may return to your ship."

"Thank you, madam president."

Walter turned and left the room to return to his Raptor.

**Battlestar Galactica**

**A week later**

"This was I know names and faces, I know who runs the black market this way if they do anything wrong we can bring them down," Lee told the Galactica's CO and the Admiral.

"Alright, you can go," Adama said waving Lee out of his office. "Admiral, what do you think?"

"While I appreciate knowing who is running the black market I'd rather it be shut down completely, but you can't win every day can you? See you around Commander.

**Battlestar Zenobia**

**Admiral Walter's personal room**

**AKA the Library**

**Admiral James Walter, President Laura Roslin, Commander Adama, Colonel Tyrol and Billy Keikeya**

"The tylliam ship needs more time," Roslin started while Admiral Walter handed out tea.

"We'll that's a luxury we don't have, we're losing pilots too quickly, we need to leave as soon as possible,"

"But we need the Tylliam,"

"We need to hunt down this raider called Scar," Walter quietly said, this caused everyone to stop and look at him. "You heard me, tell Lieutenant Thrace to draw up an attack plan."


	6. Hostages and Commanders

**Hostages and Commanders**

Will follow the rest of Scar, Sacrifice and The Captains hand.

* * *

><p><strong>Battlestar Zenobia<strong>

**Admiral Walter's personal room**

**AKA the Library**

**Admiral James Walter, President Laura Roslin, Commander Adama, Colonel Tyrol and Billy Keikeya**

"Scar's been neutralised, give Kara Thrace and Louanne Katrine my thanks Commander," Walter as per usual started the meeting with the good items on the agenda. "And we've finished the mining, so we're ready to ship out to resume the search for the 13th colony."

"We're looking at the starmap retrieved from Kobol trying to get a better idea of where we're going from here," Tyrol told them while looking up from a print-out. "But as of yet there's been no progress so far."

"Alright, Madam President, Commander, Colonel you're dismissed," Walter said with a salute before waving them out of the library.

**Battlestar Zenobia**

**Corridor**

**A few minutes later**

Adama wouldn't admit it if you asked him, but he was lost, while on board he wanted to explore the newer ship but was now lost. He was so involved in trying to find the way back that he didn't realise when he crashed into a blond haired Lieutenant.

"Sorry Lieutenant, I should have been paying attention," Adama quickly said before he recognised the blond Lieutenant, the same as the reporter who went on the Galactica, he was about to raise the alarm when he remembered that one of that model had defected to their side and was part of the Zenobia's crew.

Lieutenant D'Anna Biers watched as Adama tried to think of something else to say, she giggled briefly before calming herself. "Are you lost Commander?" she asked while loosely placing her hand on his arm. This snapped Adama out of his trance and he looked into her eyes to see an amused smile.

"Well… yes," Adama answered while slightly blushing.

"Where are you trying to go Commander?" D'Anna asked.

"The erm… starboard hanger deck," Adama said while slightly gesturing his right hand.

"Right, that's this way," with that D'Anna lead him to the hanger deck still smiling.

When they arrived he saluted the lieutenant and entered the Raptor bound for the Galactica, where he tried to tell himself that he didn't find D'Anna attractive.

**Battlestar Galactica **

**CIC**

**A Few Days Later**

"Lieutenant Valerii reporting for duty sir," Boomer said as she saluted and entered the visual range of Commander Adama. Adama looked up from the print out he was reading.

"Lieutenant, a situation has developed on board Cloud Nine, a group of terrorists have taken hostages including Captain Apollo and Billy Keikeya, they're demanding that we hand over the cylon of the same model from you that currently resides in the special brig," Adama summarised the situation for her benefit.

"And what are your orders, sir?" Boomer asked while looking at the faces of the bridge crew who were all looking at her suspiciously, she couldn't blame them, not after the last time she had been in this room, ironically the only person who wasn't on edge was the man she had shot, Adama's face was a statue of calm, as if the centre of a storm.

"I want you to fly a Raptor over and arrest the bastards, with my authorisation to shoot to kill anyone who resists," Adama quickly told her noticing that some of the officers were fingering their side arms. "Dismissed Lieutenant,"

They both saluted and Boomer left the CIC much too every ones relief.

"Bill I don't know why you did that," Saul whispered into his ear. Adama just looked back at him. "I mean Admiral Walter gave you authorisation to deal with this by any means necessary, and you pick her, come on you don't buy the whole, 'She couldn't control herself' story are you"

"Yes Colonel, I am as you said 'buying it', she is an officer who has always followed orders and deserves a chance to prove her loyalty and to be honest, I thinks that she's our best bet," Adama replied in a hushed voice to Tigh. "Lieutenant Gaeta get the terrorists on the horn,"

"Yes sir," Gaeta said while moving back to his console and pushing the necessary buttons to connect the two ships. "I've got them Commander, you're live."

"This is Adama I'm sending over Valerii for you now afterwards you will all present yourselves for arrest, is that clear?" Adama spoke in his usual calm tone.

"I'm sorry Commander that's not acceptable…" whatever else Sesha had to say was cut off as Adama interrupted her.

"I don't give a dam what you think, you're the terrorist and I'm the Commander so it's my suggestions you'll be following, is that clear," Adama was clearly angered and was just short of shouting down the line.

Sesha's voice was shaky when she responded, it was an affirmative, Adama looked up at Gaeta. "Tell Boomer that she's cleared to depart."

"Yes sir," the hesitation was clear in Gaeta's voice as he turned and authorised Boomer's raptor to take off.

**Battlestar Galactica**

**Port Hanger Deck**

**Boomer's Raptor**

Lieutenant Valerii looked around her raptor and smiled, _an actual mission, not just Galen's milk-runs, _her smile brightened at the thought of Galen Tyrol, now that Admiral Walter was in charge Liard stayed on as Galactica's deck chief, while he was a good engineer he wasn't very good at military protocol. In fact Valerii counted herself lucky that Walter hadn't promoted Cally to deck chief, she would never feel safe in a raptor that Cally'd performed maintenance on.

When Gaeta sent the order through to leave the ship she followed her perfectly rehearsed take-off pattern, when the shuttle emerged from the hanger deck she banked port towards cloud-nine, she performed a textbook landing, she hadn't made a bad landing since just before her mission to blow up the base ship.

**Cloud Nine**

**Hanger bay**

Kara Thrace watched as Boomer's Raptor touched down, she wasn't quite sure if Adama's plan was brilliant or incredibly stupid, but because it came from the _old man_ she was giving it the benefit of the doubt. Boomer stepped out of the Raptor and looked around before seeing Captain Thrace.

"Captain," Boomer saluted Kara looking up.

"Lieutenant," Kara returned the salute, Kara then proceeded to tell Boomer about the situation just as Boomer was about to leave the hanger to head for the bar Kara surprised herself by calling out. "Hey Sharon, it's good to see you back in uniform,"

Boomer smiled back and thanked her before walking towards the bar.

**Cloud Nine**

**Bar **

**Hostage Situation**

Boomer entered the Bar with her hands raised but ready to take her gun at the slightest movement, she saw Lee unconscious and bleeding out on the floor with Billy and Dee next to him, she looked up at Sesha, the terrorist ring leader, she was clearly unstable when she started laughing and crying at the illusion that Adama had given in to the terrorists.

Boomer waited for the right moment, as soon as she was just facing Sesha she whipped out her pistol and fired tranquiliser rounds at the men facing the hostages, she then turned and pointed it at Sesha who had barely blinked.

"Sesha Abinell, as a lieutenant of the Colonial fleet I hereby place you under arrest for inciting a terrorist act," as soon as Boomer finished the sentence she placed the cuffs on Sesha's hands, as soon as the cuffs closed Sesha spat at Boomer.

"Toaster bitch," Boomer looked taken back as Sesha now looked feral and animal like filled with hate and loathing and so twisted that she barely seemed human…

The next day the press releases hailed Sharon 'Boomer' Valerii as a hero and based on a formal and quite official psychiatric evidence Sesha Abinell was portrayed as an insane mad-woman, and after quite literally dragging Lee out of the bar and into the medical bay was put back onto active flight status and her relationship with Galen Tyrol was now very public and allowed because Galen was technically outside the chain of command even though they had different ranks, in her opinion life was fantastic.

**Battlestar Galactica**

**Specialist Callandra Henderson's misery**

To be brunt Cally was pissed, at Sharon for coming back, for Galen for picking her and Adama for letting her in. She already knew how to get hold of the toaster bitch, and after she removed Sharon, Galen could be hers.

**A week later**

**Boomer's Raptor **

**En route to Battlestar Pegasus**

"This is Raptor-971, I have the ball repeat I have the ball, coming in for landing," Sharon had easily fallen back into routine piloting, it was as if she'd never left. After the raptor had touched down safely she turned to her passenger Major Lee 'Apollo' Adama. "Well Major welcome to the so-called _Beast_, hope you enjoy your stay,"

Lee surprisingly smiled a bit and replied, "I'll try but keeping Kara out of trouble, impossible," just as he left the raptor he turned back. "Oh, and I never thanked you for getting my ass out of that bar before I bled out."

"You don't have to thank me, sir, it's my job," Sharon told him.

Lee nodded and left the Raptor, wherein Sharon immediately prepped to return to the Galactica.

**An Hour Later**

**Battlestar Zenobia**

**Admiral Walter's personal room**

**AKA the Library**

**Admiral James Walter (Zenobia CO), Commander Adama (Galactica CO), Commander Jonathon Smith (Logopolis CO) and Commander Ryan Bell (Challenger CO)**

"I've been going over the reports and while Garner is trying to be through I just have one thing to add, Kara Thrace's reports, that's why Lee was also given special orders by me to relieve Garner of duty if he endangers his ship," Walter told the three Commanders.

"Good, now if you'll excuse me we need to return to our ships…"

"_Admiral, report to the bridge," _The intercom flared as it delivered the message then died down, the four ship-captains all stared at each other for a second before jumping out of their seats and heading towards CIC.

When they arrived at the CIC of the newest Battlestar constructed Adama marvelled at its cleanliness, everything with white, the new model of the CIC was circular with a main table in the middle and computers along the circumference except at the point opposite the Commander's post there was a television screen shown the space outside, Walter strode to his station and became one with the ship.

"Report?"

Colonel Longman looked up from her position and told him that Garner had jumped the Pegasus away to search for his missing raptors.

"Show me,"

On the screen the scene rolls back to a few minutes and we see the Pegasus jump away.

"But sir, that's not the worst part of it, they're heading into a trap…" Colonel Longman finished.

* * *

><p>Sory it's a short one, I just thought that this is a good point to end it.<p> 


	7. Traps, Promotions, Dates and a birth

**Traps, Promotions, Dates and a Birth**

This will follow the rest of The Captain's Hand and Downloaded.

**Battlestar Pegasus **

**A few minutes earlier**

**Commander Garner's rescue mission**

"Commander Garner in following Admiral Walter's orders I am herby relieving you of Command for endangering this ship and crew," Lee told Garner. "Marines, please escort Mr Garner back to his quarters, he's no longer cleared to be on this deck, now marines!"

"Marines escort Major Adama to the brig for mutiny," Garner told the marines, who clearly looked conflicted, they obviously didn't want to cross Walter after the tribunal of the past month but they also had more respect for Garner since as far as they knew he didn't trust Cylons.

"Lieutenant Hoshi, open a com-line to the Zenobia and verify my orders and authority to relieve Garner of duty," Lee told Hoshi, who moved to follow his order.

"Belay that, marines you are now ordered to escort both major Adama and Lieutenant Hoshi to the brig, you are both under-" Apollo interrupted Garner before he could finish.

"Marines place Garner under arrest for disobeying orders from his Commander-in-chief," Apollo looked at Garner. "I'm sorry Commander but this is such an obvious trap that I can't let you go through with this, you'll get us all killed."

"Marines, this is a direct order get Lieutenant Hoshi and Major Adama off the CIC and into the brig!" the marines now had clearly chosen their side, they moved forward and dragged Hoshi and Apollo out of the room. "Now jump to the co-ordinates Mr Thornten, that's an order,"

Of course the Pegasus' crews resentment of the Galactica and her crew had won out as they took Apollo and Hoshi off the deck.

"Sorry about dragging you into this Lieutenant," Apollo told Hoshi looking down at the floor.

"No, it's okay _Major, _I-" Hoshi stopped talking as they both heard a shrieking alarm which both Apollo and Louis recognised. "Oh no," was all he could say as a nuke hit the engines, because the Pegasus was built in peace time it's hull armour was nowhere near as thick as the Galactica's, meaning that the hull could be breached a lot easier like in the battle at the Scorpia shipyards or a well-placed shot could knock out the FTLs like the current strike had done.

During the jolt the marines had let go of them, Apollo just turned to them, "Marines, I think you have better things to do?" while they didn't want to cross Garner they knew he was useless in a battle, as the marine nodded Hoshi and Apollo dashed back to the CIC. When they got there Garner was on the phone to engineering and it was clear that no-one was in charge, Lee nodded to Hoshi who moved to the FTL computer ready to jump when ready, Apollo then turned to Thornton.

"Ensign, target the nearest baseship and fire bow batteries," Apollo told him, Thornton just stared at him then snarled 'Friend of the Cylon' at him. So Lee pushed him out of the way and did it himself, at just that moment Garner looked up from the phone at Apollo.

"I have to get down there… Major you have the conn," with that Garner dashed out of the CIC, when the crew started to follow Lee's orders the battle started to go well, one of the Baseships withdrew but the others just came down harder, the Pegasus had lost its bow batteries and was pretty much dead in space just at that moment Hoshi called out that the FTLs were back online, Lee called to land the viper wings, and with that the Pegasus jumped away.

**Battlestar Zenobia**

**Five hours later**

**Admiral James Walter's office**

"Congratulations, Commander Lee 'Apollo' Adama, the Pegasus is now yours," Admiral Walter said as Adama put the rank pips on his uniform.

"Well done son, I'm proud of you," he whispered.

**Battlestar Zenobia**

**JAG office**

**Lieutenant D'Anna Biers office**

**Secretary to the JAG**

Adama had finish congratulating his son and was walking toward the JAG office with a map in hand; he was specifically looking at a part of the map which showed that had had a restaurant installed, and it looked half good, so when he offered D'Anna a chance to go she said yes.

**Colonial One**

**Madame President Laura Roslin's office**

"Well done Commander _Apollo," _the president told him, whenever she said his call-sign in that husky voice of hers his breath always caught in his throat.

"Erm… Madame President, that's not why I'm here," Lee started beginning to feel a little embarrassed.

"Then why are you here Commander?" Laura asked, trying not to get her hopes up.

"Well, you've probably heard that there's a restaurant on the Zenobia, and I was erm… wondering if you'd like to come with me as in on a date?" Lee asked starting to get nervous, until Laura smiled.

"Yes Lee, I'd love to, and you don't have to call me Madame President, what time shall we meet there?"

"About 2000 hours?"

"Great," Laura smiled again. "See you there."

**Battlestar Galactica**

**Colonial Corps of engineers**

**Colonel Galen Tyrol's office**

Galen looked down at the paper work, he was still making sure the Pegasus was fully repaired as well as trying to keep the fleet maintenance, he was about to drop off to sleep when Sharon's arms wrapped around him from behind and her head rested on his shoulder.

"How is it?" She asked turning to look him in the eye.

"A little boring, but the quarters are better," He said turning to face her. "So how long till you're back on the CAP?"

"A couple of hours," Sharon said smiling slightly. "Why what do you want to do with me?"

Both their eyes took on a mischievous quality as they started to kiss the living daylights out of each other and to take off each other's uniforms…

**Battlestar Zenobia**

**Special Installation **

**Restaurant**

**2000 hours**

Lee and Laura had met at the restaurant as planned and were quite shocked when they say Bill and D'Anna sharing a meal, but they just shrugged and started to eat their meals, they both enjoyed each overs company and before long they were kissing…

Bill and D'Anna kept glancing over at his son and the president and they both smiled and looked at each other.

"I think that my sons got the right idea," with that he moved and kissed D'Anna's lips slowly and deeply and to his surprise she kissed back…

**Battlestar Galactica **

**Bill Adama's Office**

**Aftermath of Cylon childbirth**

"So what do we do with it," Roslin asked the obvious question, to which James Walter just covered his face with his palm, both of the Adama's rolled their eyes, Baltar started to look uncomfortable and Sherman Cottle just glared at her. "What, you can't seriously suggest we let her cylon mother raise her?"

"I think that is what everyone is thinking," Walter replied looking her in the eye, and to Roslin's surprise everyone nodded and murmured agreement.

Adama looked at her, he knew that any decision that he made could affect any future he had with D'Anna, despit her being a cylon he knew deep down in his heart that he loved her. Baltar was being tormented by the head version of six, he was beginning to feel distracted by her ministrations, _no must focus, _Baltar was able to focus on Roslin and off of the enchanting siren of a cylon.

Before Roslin said anything else she looked at Apollo and saw the pleading look in her eyes, and it made her heart melt.

"Oh alright then, we let her raise her child," Laura told the others, in truth she didn't want to alienate Lee just yet, they had just got started.

**IMPORTANT AUTHORS NOTE:**

Announcing the start of my new project, another BSG/Star Trek crossover.

**New Beginnings- An Original Star Trek/BSG(2003) Crossover**

What happens when a prototype Federation Starship is thrown into another Galaxy for a rendezvous with the Galactica after the shooting of Adam? Will it herald a new era or start a war beyond the imaginings of the Cylons?

And what exactly is manipulating a whole Galaxy of coincedences?


End file.
